Reference genes for quantitative RT-PCR data in gastric tissues and cell lines

World Journal of Gastroenterology

Volumn 19, Issue 41, 2013, Pages 7121-7128

  Wisnieski, Fernanda ^a   Calcagno, Danielle Queiroz ^a   Leal, Mariana Ferreira ^a   dos Santos, Leonardo Caires ^a   Gigek, Carolina de Oliveira ^a   Chen, Elizabeth Suchi ^a   Pontes, Thaís Brilhante ^a   Assumpção, Paulo Pimentel ^b   de Assumpção, Mônica Barauna ^b   Demachki, Sâmia ^b   Burbano, Rommel Rodríguez ^b   Smith, Marília de Arruda Cardoso ^a  

^a FEDERAL UNIVERSITY OF SÃO PAULO   (Brazil)

^b FEDERAL UNIVERSITY OF PARÁ   (Brazil)

Author keywords

Gastric cancer; Gene expression; Normalization; Quantitative real time polymerase chain reaction; Reference gene

Indexed keywords

BETA 2 MICROGLOBULIN; BETA ACTIN; DNA METHYLTRANSFERASE 1; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; RNA 18S; RIBOSOMAL PROTEIN L29; RIBOSOME PROTEIN; UNCLASSIFIED DRUG;

18S RRNA GENE; ACTB GENE; ADULT; ARTICLE; B2M GENE; CONTROLLED STUDY; FEMALE; FIBROBLAST; GAPDH GENE; GENE; GENE AMPLIFICATION; GENE EXPRESSION; HUMAN; HUMAN CELL; HUMAN TISSUE; MALE; PROTEIN STABILITY; REAL TIME POLYMERASE CHAIN REACTION; RNA EXTRACTION; RPL29 GENE; STOMACH ADENOCARCINOMA; CLINICAL ARTICLE; COMPUTER PROGRAM; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

GASTRIC CANCER; GENE EXPRESSION; NORMALIZATION; QUANTITATIVE REAL-TIME POLYMERASE CHAIN REACTION; REFERENCE GENE;

ACTINS; ADENOCARCINOMA; ADULT; AGED; BETA 2-MICROGLOBULIN; CASE-CONTROL STUDIES; CELL LINE, TUMOR; COMPUTATIONAL BIOLOGY; DNA (CYTOSINE-5-)-METHYLTRANSFERASE; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASES; HUMANS; MALE; MIDDLE AGED; REAL-TIME POLYMERASE CHAIN REACTION; REFERENCE STANDARDS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; STOMACH NEOPLASMS; TUMOR MARKERS, BIOLOGICAL;

EID: 84887511874     PISSN: 10079327     EISSN: 22192840     Source Type: Journal    
DOI: 10.3748/wjg.v19.i41.7121     Document Type: Article

References (30)

1. Jemal A, Bray F, Center MM, Ferlay J, Ward E, Forman D. Global cancer statistics. CA Cancer J Clin 2011; 61: 69-90 [PMID: 21296855 DOI: 10.3322/caac.20107]
2. Crew KD, Neugut AI. Epidemiology of gastric cancer. World J Gastroenterol 2006; 12: 354-362 [PMID: 16489633]
3. Shah MA, Ajani JA. Gastric cancer--an enigmatic and heterogeneous disease. JAMA 2010; 303: 1753-1754 [PMID: 20442394 DOI: 10.1001/jama.2010.553]
4. Bustin SA. Absolute quantification of mRNA using realtime reverse transcription polymerase chain reaction assays. J Mol Endocrinol 2000; 25: 169-193 [PMID: 11013345 DOI: 10.1677/jme.0.0250169]
5. Bustin SA, Benes V, Nolan T, Pfaffl MW. Quantitative realtime RT-PCR--a perspective. J Mol Endocrinol 2005; 34: 597-601 [PMID: 15956331 DOI: 10.1677/jme.1.01755]
6. Derveaux S, Vandesompele J, Hellemans J. How to do successful gene expression analysis using real-time PCR. Methods 2010; 50: 227-230 [PMID: 19969088 DOI: 10.1016/ j.ymeth.2009.11.001]
7. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F. Accurate normalization of realtime quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 2002; 3: RESEARCH0034 [PMID: 12184808]
8. de Jonge HJ, Fehrmann RS, de Bont ES, Hofstra RM, Gerbens F, Kamps WA, de Vries EG, van der Zee AG, te Meerman GJ, ter Elst A. Evidence based selection of housekeeping genes. PLoS One 2007; 2: e898 [PMID: 17878933 DOI: 10.1371/journal.pone.0000898]
9. Ho-Pun-Cheung A, Bascoul-Mollevi C, Assenat E, Bibeau F, Boissière-Michot F, Cellier D, Ychou M, Lopez-Crapez E. Validation of an appropriate reference gene for normalization of reverse transcription-quantitative polymerase chain reaction data from rectal cancer biopsies. Anal Biochem 2009; 388: 348-350 [PMID: 19272348 DOI: 10.1016/j.ab.2009.03.001]
10. Li YL, Ye F, Hu Y, Lu WG, Xie X. Identification of suitable reference genes for gene expression studies of human serous ovarian cancer by real-time polymerase chain reaction. Anal Biochem 2009; 394: 110-116 [PMID: 19622337 DOI: 10.1016/ j.ab.2009.07.022]
11. Ohl F, Jung M, Xu C, Stephan C, Rabien A, Burkhardt M, Nitsche A, Kristiansen G, Loening SA, Radonić A, Jung K. Gene expression studies in prostate cancer tissue: which reference gene should be selected for normalization? J Mol Med (Berl) 2005; 83: 1014-1024 [PMID: 16211407 DOI: 10.1007/ s00109-005-0703-z]
12. Bustin SA, Mueller R. Real-time reverse transcription PCR (qRT-PCR) and its potential use in clinical diagnosis. Clin Sci (Lond) 2005; 109: 365-379 [PMID: 16171460 DOI: 10.1042/ CS20050086]
13. Hruz T, Wyss M, Docquier M, Pfaffl MW, Masanetz S, Borghi L, Verbrugghe P, Kalaydjieva L, Bleuler S, Laule O, Descombes P, Gruissem W, Zimmermann P. RefGenes: identification of reliable and condition specific reference genes for RT-qPCR data normalization. BMC Genomics 2011; 12: 156 [PMID: 21418615 DOI: 10.1186/1471-2164-12-156]
14. Rho HW, Lee BC, Choi ES, Choi IJ, Lee YS, Goh SH. Identification of valid reference genes for gene expression studies of human stomach cancer by reverse transcription-qPCR. BMC Cancer 2010; 10: 240 [PMID: 20507635 DOI: 10.1186/14 71-2407-10-240]
15. Leal MF, Martins do Nascimento JL, da Silva CE, Vita Lamarão MF, Calcagno DQ, Khayat AS, Assumpção PP, Cabral IR, de Arruda Cardoso Smith M, Burbano RR. Establishment and conventional cytogenetic characterization of three gastric cancer cell lines. Cancer Genet Cytogenet 2009; 195: 85-91 [PMID: 19837275 DOI: 10.1016/j.cancergencyto.2009.04.020]
16. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T) Method. Methods 2001; 25: 402-408 [PMID: 11846609 DOI: 10.1006/meth.2001.1262]
17. Andersen CL, Jensen JL, Ørntoft TF. Normalization of realtime quantitative reverse transcription-PCR data: a modelbased variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res 2004; 64: 5245-5250 [PMID: 15289330 DOI: 10.1158/0008-5472.CAN-04-0496]
18. Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP. Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper--Excel-based tool using pair-wise correlations. Biotechnol Lett 2004; 26: 509-515 [PMID: 15127793 DOI: 10.1023/B:BILE.0000019559.8 4305.47]
19. Rubie C, Kempf K, Hans J, Su T, Tilton B, Georg T, Brittner B, Ludwig B, Schilling M. Housekeeping gene variability in normal and cancerous colorectal, pancreatic, esophageal, gastric and hepatic tissues. Mol Cell Probes 2005; 19: 101-109 [PMID: 15680211 DOI: 10.1016/j.mcp.2004.10.001]
20. Lyng MB, Laenkholm AV, Pallisgaard N, Ditzel HJ. Identification of genes for normalization of real-time RT-PCR data in breast carcinomas. BMC Cancer 2008; 8: 20 [PMID: 18211679 DOI: 10.1186/1471-2407-8-20]
21. Fu J, Bian L, Zhao L, Dong Z, Gao X, Luan H, Sun Y, Song H. Identification of genes for normalization of quantitative realtime PCR data in ovarian tissues. Acta Biochim Biophys Sin (Shanghai) 2010; 42: 568-574 [PMID: 20705598 DOI: 10.1093/ abbs/gmq062]
22. Shen Y, Li Y, Ye F, Wang F, Lu W, Xie X. Identification of suitable reference genes for measurement of gene expression in human cervical tissues. Anal Biochem 2010; 405: 224-229 [PMID: 20599650 DOI: 10.1016/j.ab.2010.06.029]
23. Wang Q, Ishikawa T, Michiue T, Zhu BL, Guan DW, Maeda H. Stability of endogenous reference genes in postmortem human brains for normalization of quantitative real-time PCR data: comprehensive evaluation using geNorm, Norm-Finder, and BestKeeper. Int J Legal Med 2012; 126: 943-952 [PMID: 23010907 DOI: 10.1007/s00414-012-0774-7]
24. Batista dos Santos SE, Rodrigues JD, Ribeiro-dos-Santos AK, Zago MA. Differential contribution of indigenous men and women to the formation of an urban population in the Amazon region as revealed by mtDNA and Y-DNA. Am J Phys Anthropol 1999; 109: 175-180 [PMID: 10378456 DOI: 10.1002/(SICI)1096-8644(199906)109]
25. Solanas M, Moral R, Escrich E. Unsuitability of using ribosomal RNA as loading control for Northern blot analyses related to the imbalance between messenger and ribosomal RNA content in rat mammary tumors. Anal Biochem 2001; 288: 99-102 [PMID: 11141312 DOI: 10.1006/abio.2000.4889]
26. Tricarico C, Pinzani P, Bianchi S, Paglierani M, Distante V, Pazzagli M, Bustin SA, Orlando C. Quantitative real-time reverse transcription polymerase chain reaction: normalization to rRNA or single housekeeping genes is inappropriate for human tissue biopsies. Anal Biochem 2002; 309: 293-300 [PMID: 12413463 DOI: 10.1016/S0003-2697(02)00311-1]
27. Radonić A, Thulke S, Mackay IM, Landt O, Siegert W, Nitsche A. Guideline to reference gene selection for quantitative real-time PCR. Biochem Biophys Res Commun 2004; 313: 856-862 [PMID: 14706621 DOI: 10.1016/j.bbrc.2003.11.177]
28. Mogal A, Abdulkadir SA. Effects of Histone Deacetylase Inhibitor (HDACi); Trichostatin-A (TSA) on the expression of housekeeping genes. Mol Cell Probes 2006; 20: 81-86 [PMID: 16326072 DOI: 10.1016/j.mcp.2005.09.008]
29. Lauren P. The two histological main types of gastric carcinoma: diffuse and so-called intestinal-type carcinoma. An attempt at a histo-clinical classification. Acta Pathol Microbiol Scand 1965; 64: 31-49 [PMID: 14320675]
30. Washington K. 7th edition of the AJCC cancer staging manual: stomach. Ann Surg Oncol 2010; 17: 3077-3079 [PMID: 20882416 DOI: 10.1245/s10434-010-1362-z]